ArticleBMC genetics2009
Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.
Article in BMC genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees.Evolutionary applications · 2016Article
- Investigating highly replicated asthma genes as candidate genes for allergic rhinitis.BMC medical genetics · 2013Article
- Pooling/bootstrap-based GWAS (pbGWAS) identifies new loci modifying the age of onset in PSEN1 p.Glu280Ala Alzheimer's disease.Molecular psychiatry · 2013Article
- Genome-wide association study identifies PERLD1 as asthma candidate gene.BMC medical genetics · 2011Article
- Genetic predisposition for atopy and allergic rhinitis in the Singapore Chinese population.Asia Pacific allergy · 2011Article
- Genome-wide association study for atopy and allergic rhinitis in a Singapore Chinese population.PloS one · 2011Article
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2 authors.
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Abstract
backgroundThe use of pooled DNA on SNP microarrays (SNP-MaP) has been shown to be a cost effective and rapid manner to perform whole-genome association evaluations. While the accuracy of SNP-MaP was extensively evaluated on the early Affymetrix 10 k and 100 k platforms, there have not been as many similarly comprehensive studies on more recent platforms. In the present study, we used the data generated from the full Affymetrix 500 k SNP set together with the polynomial-based probe-specific correction (PPC) to derive allele frequency estimates. These estimates were compared to genotyping results of the same individuals on the same platform, as the basis to evaluate the reliability and accuracy of pooled genotyping on these high-throughput platforms. We subsequently extended this comparison to the new SNP6.0 platform capable of genotyping 1.8 million genetic variants.
resultsWe showed that pooled genotyping on the 500 k platform performed as well as those previously shown on the relatively lower throughput 10 k and 100 k array sets, with high levels of accuracy (correlation coefficient: 0.988) and low median error (0.036) in allele frequency estimates. Similar results were also obtained from the SNP6.0 array set. A novel pooling strategy of overlapping sub-pools was attempted and comparison of estimated allele frequencies showed this strategy to be as reliable as replicate pools. The importance of an appropriate reference genotyping data set for the application of the PPC algorithm was also evaluated; reference samples with similar ethnic background to the pooled samples were found to improve estimation of allele frequencies.
conclusionWe conclude that use of the PPC algorithm to estimate allele frequencies obtained from pooled genotyping on the high throughput 500 k and SNP6.0 platforms is highly accurate and reproducible especially when a suitable reference sample set is used to estimate the beta values for PPC.
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